Repository 'stacks_rxstacks'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/stacks_rxstacks

Changeset 8:1919e1ecb90d (2017-04-27)
Previous changeset 7:f4a15ab64300 (2017-04-07) Next changeset 9:2360d8cf42f7 (2017-05-21)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
modified:
macros.xml
stacks_rxstacks.xml
added:
test-data/demultiplexed/PopA_01.1.fq.gzip
test-data/denovo_map/popmap_cstacks.tsv
test-data/procrad/R1.fq.gzip
test-data/ustacks/ustacks.out
b
diff -r f4a15ab64300 -r 1919e1ecb90d macros.xml
--- a/macros.xml Fri Apr 07 11:48:48 2017 -0400
+++ b/macros.xml Thu Apr 27 04:19:22 2017 -0400
[
@@ -2,14 +2,14 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.42">stacks</requirement>
+            <requirement type="package" version="1.46">stacks</requirement>
             <requirement type="package" version="1.2.10">velvet</requirement>
-            <container type="docker">quay.io/biocontainers/stacks:1.42--2</container>
+            <requirement type="package" version="1.1">stacks_summary</requirement>
             <yield/>
         </requirements>
     </xml>
 
-    <token name="@WRAPPER_VERSION@">1.42</token>
+    <token name="@WRAPPER_VERSION@">1.46</token>
 
     <xml name="stdio">
         <stdio>
@@ -90,6 +90,7 @@
         <option value="bsaHI">bsaHI</option>
         <option value="hpaII">hpaII</option>
         <option value="ncoI">ncoI</option>
+        <option value="ApaLI">ApaLI</option>
     </xml>
 
     <xml name="cross_types">
@@ -100,6 +101,19 @@
         <option value="GEN">GEN (generic, unspecific to any map type)</option>
     </xml>
 
+    <token name="@CLEAN_EXT@">
+        <![CDATA[
+        #from os.path import splitext
+        #import re
+        #def clean_ext($identifier)
+            #while $identifier.endswith(('.1', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam'))
+                #set $identifier = splitext($identifier)[0]
+            #end while
+$identifier#slurp
+        #end def
+        ]]>
+    </token>
+
     <token name="@NORM_GENOTYPES_OUTPUT_LIGHT@">
         <![CDATA[
         ## We need to do this as the output file names contains the value of an option (min progeny)
b
diff -r f4a15ab64300 -r 1919e1ecb90d stacks_rxstacks.xml
--- a/stacks_rxstacks.xml Fri Apr 07 11:48:48 2017 -0400
+++ b/stacks_rxstacks.xml Thu Apr 27 04:19:22 2017 -0400
b
@@ -11,12 +11,12 @@
 
         &&
 
-        #for $input_file in $input_col:
+        #for $input_file in $input_col
             #set $ext = ""
-            #if not str($input_file.element_identifier).endswith('.tsv'):
+            #if not str($input_file.element_identifier).endswith('.tsv')
                 #set $ext = ".tsv"
             #end if
-            ln -s "${input_file}" "stacks_inputs/${input_file.element_identifier}${ext}" &&
+            ln -s '${input_file}' 'stacks_inputs/${input_file.element_identifier}${ext}' &&
         #end for
 
         rxstacks
@@ -28,32 +28,32 @@
             ## Batch description
             -b 1
 
-            #if str($options_filtering.lnl):
+            #if str($options_filtering.lnl)
                 --lnl_filter
                 --lnl_lim $options_filtering.lnl
             #end if
 
             $options_filtering.lnl_dist
 
-            #if str($options_filtering.conf):
+            #if str($options_filtering.conf)
                 --conf_filter
                 --conf_lim $options_filtering.conf
             #end if
 
-            #if $options_filtering.prune.prune_haplo:
+            #if $options_filtering.prune.prune_haplo == "yes"
                 --prune_haplo
-                #if str($options_filtering.prune.max_haplo):
+                #if str($options_filtering.prune.max_haplo)
                     --max_haplo $options_filtering.prune.max_haplo
                 #end if
             #end if
 
             ## snp_model
-            #if str( $snp_options.select_model.model_type) == "bounded":
+            #if str( $snp_options.select_model.model_type) == "bounded"
                 --model_type bounded
                 --bound_low $snp_options.select_model.bound_low
                 --bound_high $snp_options.select_model.bound_high
                 --alpha $snp_options.select_model.alpha
-            #else if str( $snp_options.select_model.model_type) == "snp":
+            #else if str( $snp_options.select_model.model_type) == "snp"
                 --model_type snp
                 --alpha $snp_options.select_model.alpha
             #else
@@ -73,9 +73,12 @@
             <param name="conf" type="float" value="0.75" optional="true" argument="--conf_lim" min="0.0" max="1.0" label="Proportion of loci in population that must be confounded relative to the catalog locus (between 0.0 and 1.0)."/>
 
             <conditional name="prune">
-                <param name="prune_haplo" argument="--prune_haplo" type="boolean" checked="false" label="Prune out non-biological haplotypes unlikely to occur in the population." />
-                <when value="false"></when>
-                <when value="true">
+                <param name="prune_haplo" argument="--prune_haplo" type="select" label="Prune out non-biological haplotypes unlikely to occur in the population.">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">Yes</option>
+                </param>
+                <when value="no"/>
+                <when value="yes">
                     <param name="max_haplo" argument="--max_haplo" type="integer" value="" optional="true" label="Only consider haplotypes for pruning if they occur in fewer than this value."/>
                 </when>
             </conditional>
@@ -130,7 +133,7 @@
             </param>
             <param name="options_filtering|lnl" value="-10.0" />
             <param name="options_filtering|lnl_dist" value="true" />
-            <param name="options_filtering|prune_haplo" value="true" />
+            <param name="options_filtering|prune_haplo" value="yes" />
             <param name="options_filtering|max_haplo" value="1" />
 
             <output name="output_log">
b
diff -r f4a15ab64300 -r 1919e1ecb90d test-data/demultiplexed/PopA_01.1.fq.gzip
b
Binary file test-data/demultiplexed/PopA_01.1.fq.gzip has changed
b
diff -r f4a15ab64300 -r 1919e1ecb90d test-data/denovo_map/popmap_cstacks.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/denovo_map/popmap_cstacks.tsv Thu Apr 27 04:19:22 2017 -0400
b
@@ -0,0 +1,1 @@
+PopA_01 myPopA
b
diff -r f4a15ab64300 -r 1919e1ecb90d test-data/procrad/R1.fq.gzip
b
Binary file test-data/procrad/R1.fq.gzip has changed
b
diff -r f4a15ab64300 -r 1919e1ecb90d test-data/ustacks/ustacks.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ustacks/ustacks.out Thu Apr 27 04:19:22 2017 -0400
b
@@ -0,0 +1,41 @@
+ustacks parameters selected:
+  Sample ID: 1
+  Min depth of coverage to create a stack: 2
+  Max distance allowed between stacks: 2
+  Max distance allowed to align secondary reads: 4
+  Max number of stacks allowed per de novo locus: 3
+  Deleveraging algorithm: disabled
+  Removal algorithm: enabled
+  Model type: SNP
+  Alpha significance level for model: 0.05
+  Gapped alignments: disabled
+Parsing stacks_inputs/PopA_01.fq
+Loading RAD-Tags...done
+Loaded 66 RAD-Tags.
+  Inserted 7 elements into the RAD-Tags hash map.
+  0 reads contained uncalled nucleotides that were modified.
+4 initial stacks were populated; 3 stacks were set aside as secondary reads.
+Initial coverage mean: 15.75; Std Dev: 7.46241; Max: 27
+Deleveraging trigger: 23; Removal trigger: 31
+Calculating distance for removing repetitive stacks.
+  Distance allowed between stacks: 1; searching with a k-mer length of 47 (48 k-mers per read); 1 k-mer hits required.
+Removing repetitive stacks.
+  Removed 0 stacks.
+  4 stacks remain for merging.
+Post-Repeat Removal, coverage depth Mean: 15.75; Std Dev: 7.46241; Max: 27
+Calculating distance between stacks...
+  Distance allowed between stacks: 2; searching with a k-mer length of 31 (64 k-mers per read); 2 k-mer hits required.
+Merging stacks, maximum allowed distance: 2 nucleotide(s)
+  4 stacks merged into 3 loci; deleveraged 0 loci; blacklisted 0 loci.
+After merging, coverage depth Mean: 21; Std Dev: 4.24264; Max: 27
+Merging remainder radtags
+  3 remainder sequences left to merge.
+  Distance allowed between stacks: 4; searching with a k-mer length of 17 (78 k-mers per read); 10 k-mer hits required.
+  Matched 3 remainder reads; unable to match 0 remainder reads.
+After remainders merged, coverage depth Mean: 22; Std Dev: 4.32049; Max: 28
+Calling final consensus sequences, invoking SNP-calling model...
+Number of utilized reads: 66
+Writing loci, SNPs, and alleles to 'stacks_outputs/'...
+  Refetching sequencing IDs from stacks_inputs/PopA_01.fq... read 66 sequence IDs.
+done.
+ustacks is done.